Brent Pedersen

hi, this seems pretty feasible. Does anyone have other metrics to include? I can track (in addition to median), max, min and percentiles.

Hi, this is something that should be done with the d4 output and then the d4 utils or a simple python script.

see here: https://github.com/38/d4-format#run-stat-on-a-d4-file

I would accept a PR add this, but probably won't add it myself. You can run `mosdepth` on a 30X genome in < 10 minutes so extracting individual chromosomes is...

thanks for the clear report. not sure why someone hasn't noticed this before. I have a fix for this, where there's a '-' in the chromsome name. It still won't...

yeah, for the bed file, i think your solution is the best way to go. I'll make a new release with the other fix by next week.

thanks for the feedback. (I didn't know about bg2bw). the per-base bed is so large that parsing it takes as much CPU time as generating it. so even if I...

I can see why one could want `-pc`, but why use `-fs` ?

this is fairly easy to implement after developing [bigwig-nim](https://github.com/brentp/bigwig-nim), but it substantially increases the memory use. I am trying to figure out how to mitigate that. meanwhile, it's possible to...

can you show the output of `samtools view $bam chr1:1-10000` for the bam in question?